Estimating the Y-DNA and autosomal admixtures of Yamnaya samples

Robert6 said:
It is too early to consider R1a as a haplogroup of Yamna culture, let's wait for ancient Y-dna
Click to expand...

Unless you want to argue that the Indo-Europeans left little genetic trace in Iran, India and Eastern Europe, or unless you think Yamnaya culture wasn't Indo-European, I don't think it's premature to consider R1a to be the main Y haplogroup of Yamnaya culture.
 
arvistro said:
Well, at least they could share facts. Blah, blah - 7 sceletons from x years ago from this geographic location. 3 had R1a, 1 I2, 2 N with xyz subclades.
No harm to career and million info for us to discuss another couple of months :)
Click to expand...

What every graduate student wants is to be able to write their thesis on material that wasn't previously available to the public, although they sometimes have trouble getting that because such material is also coveted by their professors, who often face a "publish or perish" dilemma. So releasing the raw data would in fact have a negative impact on careers. We may not like the fact that members of academia consider a little thing like their career future to be more important than the curiosity of hobbyists, but that's how the academic world works.
 
Aberdeen said:
Unless you want to argue that the Indo-Europeans left little genetic trace in Iran, India and Eastern Europe, or unless you think Yamnaya culture wasn't Indo-European, I don't think it's premature to consider R1a to be the main Y haplogroup of Yamnaya culture.
Click to expand...
Because I think that Yamna was most possibly proto-Indo-Iranian culture,
and there is almost no R1a-Z93 in Yamna territories, for that reason I think that proto-Indo-Iranians left little genetic trace in India
 
Aberdeen said:
What every graduate student wants is to be able to write their thesis on material that wasn't previously available to the public, although they sometimes have trouble getting that because such material is also coveted by their professors, who often face a "publish or perish" dilemma. So releasing the raw data would in fact have a negative impact on careers. We may not like the fact that members of academia consider a little thing like their career future to be more important than the curiosity of hobbyists, but that's how the academic world works.
Click to expand...
That does not sound very Grigori Perelman to me......
http://en.wikipedia.org/wiki/Grigori_Perelman
In August 2006, Perelman was awarded the Fields Medal[1] for "his contributions to geometry and his revolutionary insights into the analytical and geometric structure of the Ricci flow." Perelman declined to accept the award or to appear at the congress, stating: "I'm not interested in money or fame; I don't want to be on display like an animal in a zoo."[2] On 22 December 2006, the scientific journal Science recognized Perelman's proof of the Poincaré conjecture as the scientific "Breakthrough of the Year", the first such recognition in the area of mathematics.[3]

On 18 March 2010, it was announced that he had met the criteria to receive the first Clay Millennium Prize[4] for resolution of the Poincaré conjecture. On 1 July 2010, he turned down the prize of one million dollars, saying that he considered the award unfair and that his contribution to solving the Poincaré conjecture was no greater than that of Richard Hamilton, the mathematician who pioneered Ricci flow with the aim of attacking the conjecture.[5][6] He additionally turned down the prestigious prize of the European Mathematical Society.[7]
 
I think out of the Yamnaya mtDNA we do have the distinct clades are I,J,K,N1a,T1a,T2a1b,U2e,U5a1,W, and X

[TABLE="width: 256"]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]N1a[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]?[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U5[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]X[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T1a[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]J[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]K[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U/K[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U5a1[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]W[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Russia[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T2a1b1a[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U2e1a[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U5a1[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Bulgaria[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]K[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]I[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]H[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Moldova[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]U[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T1a[/TD]
[/TR]
[TR]
[TD="class: xl65, width: 64"]Yamnaya[/TD]
[TD="class: xl65, width: 64"]Ukraine[/TD]
[TD="class: xl65, width: 64"]5000–4500 y.a.[/TD]
[TD="class: xl65, width: 64"]T1[/TD]
[/TR]
[/TABLE]
 
Robert6 said:
Because I think that Yamna was most possibly proto-Indo-Iranian culture,
and there is almost no R1a-Z93 in Yamna territories, for that reason I think that proto-Indo-Iranians left little genetic trace in India
Click to expand...

Okaaay. I guess that's one way you could look at it.
 
arvistro said:
That does not sound very Grigori Perelman to me......
http://en.wikipedia.org/wiki/Grigori_Perelman
In August 2006, Perelman was awarded the Fields Medal[1] for "his contributions to geometry and his revolutionary insights into the analytical and geometric structure of the Ricci flow." Perelman declined to accept the award or to appear at the congress, stating: "I'm not interested in money or fame; I don't want to be on display like an animal in a zoo."[2] On 22 December 2006, the scientific journal Science recognized Perelman's proof of the Poincaré conjecture as the scientific "Breakthrough of the Year", the first such recognition in the area of mathematics.[3]

On 18 March 2010, it was announced that he had met the criteria to receive the first Clay Millennium Prize[4] for resolution of the Poincaré conjecture. On 1 July 2010, he turned down the prize of one million dollars, saying that he considered the award unfair and that his contribution to solving the Poincaré conjecture was no greater than that of Richard Hamilton, the mathematician who pioneered Ricci flow with the aim of attacking the conjecture.[5][6] He additionally turned down the prestigious prize of the European Mathematical Society.[7]
Click to expand...

That individual may be a bit of an anomaly, even in the world of mathematics. And mathematicians are generally considered to be a bit different when compared to other academics. And even when dealing with a mathematician who was willing to give up a million dollars as a matter of principal, you might have a different response if you tried to get your hands on his data.
 
I took the Yamnaya mtDNA and combined it with all of the other aDNA tested so far and grouped it by haplogroup, then I sorted it by date. I'll add mtDNA J & K later.

ZB5cQmc.jpg
 
I'm in agreement with Maciamo. Yamna was a fusion culture. It was located enough North to protect HGs against being overrun by EEF, but not too far North not to be in contact. Creating Yamna and consequent Corded culture was a long process, probably 1 or 2 thousand years, till new blend of "Farmers of the North" was created. Pretty much on equal genetic footing of farmers to hunters.

Angela will be right too, that picture we'll receive from the paper will be unclear, and it will bring more questions than answers. I hope, we are wrong, and paper will be rich in samples through time periods and locations, showing the full picture.

The Northern regions of Yamna and younger periods should be rich in R1a, probably some I2 in the South. When I look at recent numbers for admixtures, the ratio of 70% WHG to 30% ANE makes most sense for all IE who expanded into Europe, most likely from Yamna. However it could have been a big difference between West Yamna and East Yamna horizont where almost pure ANE could have resided, giving start to R1a Z93, the steppe herders, Indo-Iranians.

In the South by the Black Sea we should see more and more EEF, radiating from Cucuteni over millenia. By Corded period we should see similar ratios of admixtures as today in these areas.
More farmer's haplogroups will be located in the South and West Yamna, G, E and J.
Yamna lasted 1,500 years. Long enough to be different genetically at the beginning than at the end.
 
What I just learned that is really interesting is that the red ochre burials of the Yamna was a custom that Neanderthals also practiced with their dead.
 
This works I think

sKdhEju.png
 
@motzart,

I think I might have understood what you did in the post above, but can you just give more details?
Is light blue the same thing we call WHG? If so you correlated it with R1A, I, R1B? Because where there are a lot of those groups there is also portion of WHG? (as in "No R1a/R1b without WHG component")?
Similarly you did for the others? The red circle is samish as EEF? So, there is no (or exceptionally rare) R1A, R1B, G2A without farming?
The yellowish circle is what? ANE? And ANE surprisingly merges only J2A and R1A? Why not R1B or N1C? Because there are R1B/N1C rich populations without ANE?

What are those colors for N1, E1B and J1? Also if we take N1C out of total N1 circle would it join the ANE/WHG circle? Meaning initial N1 careers might only hold this dark blue stuff, but when N1C1 was born they held also ANE/WHG?

Sorry for many questions. I just enjoyed your work and want to learn more and if I get it correct.
 
arvistro said:
@motzart,

I think I might have understood what you did in the post above, but can you just give more details?
Is light blue the same thing we call WHG? If so you correlated it with R1A, I, R1B? Because where there are a lot of those groups there is also portion of WHG? (as in "No R1a/R1b without WHG component")?
Similarly you did for the others? The red circle is samish as EEF? So, there is no (or exceptionally rare) R1A, R1B, G2A without farming?
The yellowish circle is what? ANE? And ANE surprisingly merges only J2A and R1A? Why not R1B or N1C? Because there are R1B/N1C rich populations without ANE?

What are those colors for N1, E1B and J1? Also if we take N1C out of total N1 circle would it join the ANE/WHG circle? Meaning initial N1 careers might only hold this dark blue stuff, but when N1C1 was born they held also ANE/WHG?

Sorry for many questions. I just enjoyed your work and want to learn more and if I get it correct.
Click to expand...

FYI, that is not his work. These are the graphs from Lazaridis et al. that I edited last year and posted on the forum. Motzart just reposted it here.

To answer your questions, yes blue represents WHG, pink EEF and beige ANE.

The circles attempt to match these admixtures with Y-haplogroups, but looking at the region of origin of the haplogroups. That's why J2 is matched to ANE as it originated around Anatolia and Iran. It doesn't make sense if you look at other places with high percentages of J2 caused by a founder effect, like Crete or Sicily. I personally disagree with this approach as it makes it look like ANE originated with J2 people, which isn't the case. It's simply because the Indo-Europeans (eg. Hittites, Mitanni, Persians, Iranians, Scythians, Kurds) invaded Iran and Anatolia that these regions now have significant levels of ANE.

In Europe ANE overlaps with N1c1 (due to intermixing with R1a populations), but that is not true for all haplogroup N1.
 
Thanks Maciamo. Of course, the more I understand, the more questions :)
1. On relating WHG to both R groups (I simply don't know that is why I ask). Is WHG admixture always present for R1A & R1B populations (say R1B in Africa, or R1A in India)?
2. Same question for EEF?
3. Relating ANE to R1A I think seems straightforward on little that I know. But why is R1B outside ANE circle?
 
arvistro said:
Thanks Maciamo. Of course, the more I understand, the more questions :)
1. On relating WHG to both R groups (I simply don't know that is why I ask). Is WHG admixture always present for R1A & R1B populations (say R1B in Africa, or R1A in India)?
2. Same question for EEF?
3. Relating ANE to R1A I think seems straightforward on little that I know. But why is R1B outside ANE circle?
Click to expand...

Be it in India, Central Asia, Siberia or even Mongolia, there is always WHG and ANE admixture wherever R1a1a and R1b1a (M269 or M73) are found. However that is not true for the African R1b1c (V88), perhaps because it was too diluted on the way, or because R1b people did not acquire WHG until they mixed with the aboriginal Steppe people (R1a).

You can see by yourself in the admixture above in which populations the blue, pink and beige admixtures are present.
 
LeBrok:When I look at recent numbers for admixtures, the ratio of 70% WHG to 30% ANE makes most sense for all IE who expanded into Europe, most likely from Yamna.
Click to expand...

How do you get from Yamnaya can be modeled as 50% Ancient Karelian/50% modern Armenian, and Corded Ware is 75% Yamnaya to this? Unless you think that most of the people speaking Indo-European languages who moved into Europe proper (or at least Northern Europe) were actually Indo-Europeanized Karelians?
 
arvistro said:
But why is not r1b in ANE circle then?
Click to expand...

Take a look at the Basque admixture, they are about as homogenous as a population gets in terms of Y DNA, 85% R1b. If the original R1b entrants to Europe contained any of the beige admixture we would see it there even in some tiny trace, but we don't. The Basques are about 50/50 of the pink and light blue admixture which is why placing them in the Venn diagram between those two groups works so perfectly. Contrary to what Maciamo statead I did not intend for J2 to represent ANE, the term ANE is really just a catch all for all the European DNA we can't attibute to EEF or WHG (or Oetzi-Loschbour/Motala). All of the population admixtures listed there contain the beige admixture on par closely with the amount of J2 Y DNA they posess, in the absence of J2 the existence of R1a contributes a small amout. This is why we can see the beige admixture in Scots and Icelanders who do have R1a vs non in the Basques who have no R1a.

The question posed was what we believe the genetic make up of the Yamna were, you can see from the mtDNA tables I made that there was a lot of the same mtDNA in the Yamna that existed in the Neolithic cultures of Europe. This is a lot of support for them containing high levels of EEF. Wether it is directly from an eastward expansion of Neolithic farmers, or a Northward expansion of Neolithic farmers from the same origin as the European ones is hard to pinpoint but I would say the latter is more likely.
 
Aberdeen said:
I don't think that R1a Corded Ware presents a problem, since I see them as being part of the "ancient Karelian-like" population - N1c seems to have arrived somewhat later. My point is that if we see R1b as an IE phenomenon, how do we explain the somewhat geographic specific diversity of subclades? I think we have to either see the diversity as very recent or see R1b as being in Europe for much longer than we have any evidence for. And I'm not personally a fan of either explanation.
Click to expand...


I'm not sure why this is an issue? Isn't R1a-M458 almost exclusively NE European/N Russian (aka Slavic) except when we see a light distribution in the Balkans from Slavic migration?

P312 - Celtic/Celtiberian/Gaulish
U106- Germanic
U152 - Possibly Italic
L23/L51 - Illyrian/IE Greek/Italic(?)

Several papers have suggested both R1b, and R1a both experienced rapid expansion. The oldest branchings of R1b (xL389) are in India and Iran, and never found in the west. These were nomadic pastoralists. R1b need not have expanded in India for it to have been classified as part of PIE, especially if the earliest tribes were not innovators of farming, many lineages would have just died out.
 
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